Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) More...

#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>

Inheritance diagram for SignalToNoiseEstimatorMedian< Container >:

Collaboration diagram for SignalToNoiseEstimatorMedian< Container >:

Public Types
enum	IntensityThresholdCalculation { MANUAL = -1 , AUTOMAXBYSTDEV = 0 , AUTOMAXBYPERCENT = 1 }
	method to use for estimating the maximal intensity that is used for histogram calculation More...

typedef SignalToNoiseEstimator< Container >::PeakIterator	PeakIterator

typedef SignalToNoiseEstimator< Container >::PeakType	PeakType

typedef SignalToNoiseEstimator< Container >::GaussianEstimate	GaussianEstimate

Public Types inherited from SignalToNoiseEstimator< MSSpectrum >
typedef Container::const_iterator	PeakIterator

typedef PeakIterator::value_type	PeakType

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	SignalToNoiseEstimatorMedian ()
	default constructor More...

	SignalToNoiseEstimatorMedian (const SignalToNoiseEstimatorMedian &source)
	Copy Constructor. More...

Public Member Functions inherited from SignalToNoiseEstimator< MSSpectrum >
	SignalToNoiseEstimator ()
	Constructor. More...

	SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
	Copy constructor. More...

SignalToNoiseEstimator &	operator= (const SignalToNoiseEstimator &source)
	Assignment operator. More...

	~SignalToNoiseEstimator () override
	Destructor. More...

virtual void	init (const MSSpectrum &c)
	Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More...

virtual double	getSignalToNoise (const Size index) const

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Assignment
double	max_intensity_
	maximal intensity considered during binning (values above get discarded) More...

double	auto_max_stdev_Factor_
	parameter for initial automatic estimation of "max_intensity_": a stdev multiplier More...

double	auto_max_percentile_
	parameter for initial automatic estimation of "max_intensity_" percentile or a stdev More...

int	auto_mode_
	determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1 More...

double	win_len_
	range of data points which belong to a window in Thomson More...

int	bin_count_
	number of bins in the histogram More...

int	min_required_elements_
	minimal number of elements a window needs to cover to be used More...

double	noise_for_empty_window_

bool	write_log_messages_

double	sparse_window_percent_

double	histogram_oob_percent_

SignalToNoiseEstimatorMedian &	operator= (const SignalToNoiseEstimatorMedian &source)

	~SignalToNoiseEstimatorMedian () override
	Destructor. More...

double	getSparseWindowPercent () const
	Returns how many percent of the windows were sparse. More...

double	getHistogramRightmostPercent () const
	Returns the percentage where the median was found in the rightmost bin. More...

void	computeSTN_ (const Container &c) override

void	updateMembers_ () override
	overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from SignalToNoiseEstimator< MSSpectrum >
virtual void	computeSTN_ (const MSSpectrum &c)=0
	computes the S/N values when init() is called More...

GaussianEstimate	estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
	calculate mean & stdev of intensities of a spectrum More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from SignalToNoiseEstimator< MSSpectrum >
std::vector< double >	stn_estimates_
	stores the noise estimate for each peak More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimatorMedian< Container >

Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)

For each datapoint in the given scan, we collect a range of data points around it (param: win_len). The noise for a datapoint is estimated to be the median of the intensities of the current window. If the number of elements in the current window is not sufficient (param: MinReqElements), the noise level is set to a default value (param: noise_for_empty_window). The whole computation is histogram based, so the user will need to supply a number of bins (param: bin_count), which determines the level of error and runtime. The maximal intensity for a datapoint to be included in the histogram can be either determined automatically (params: AutoMaxIntensity, auto_mode) by two different methods or can be set directly by the user (param: max_intensity). If the (estimated) max_intensity value is too low and the median is found to be in the last (&highest) bin, a warning will be given. In this case you should increase max_intensity (and optionally the bin_count).

Changing any of the parameters will invalidate the S/N values (which will invoke a recomputation on the next request).

Note: If more than 20 percent of windows have less than min_required_elements of elements, a warning is issued to OPENMS_LOG_WARN and noise estimates in those windows are set to the constant noise_for_empty_window.; If more than 1 percent of median estimations had to rely on the last(=rightmost) bin (which gives an unreliable result), a warning is issued to OPENMS_LOG_WARN. In this case you should increase max_intensity (and optionally the bin_count).; You can disable logging this error by setting write_log_messages and read out the values

Parameters of this class are:

Name	Type	Default	Restrictions	Description
max_intensity	int	-1	min: -1	maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.
auto_max_stdev_factor	float	3.0	min: 0.0 max: 999.0	parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
auto_max_percentile	int	95	min: 0 max: 100	parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
auto_mode	int	0	min: -1 max: 1	method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
win_len	float	200.0	min: 1.0	window length in Thomson
bin_count	int	30	min: 3	number of bins for intensity values
min_required_elements	int	10	min: 1	minimum number of elements required in a window (otherwise it is considered sparse)
noise_for_empty_window	float	1.0e20		noise value used for sparse windows
write_log_messages	string	true	true, false	Write out log messages in case of sparse windows or median in rightmost histogram bin

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

◆ GaussianEstimate

typedef SignalToNoiseEstimator<Container>::GaussianEstimate GaussianEstimate

◆ PeakIterator

typedef SignalToNoiseEstimator<Container>::PeakIterator PeakIterator

◆ PeakType

typedef SignalToNoiseEstimator<Container>::PeakType PeakType

Member Enumeration Documentation

◆ IntensityThresholdCalculation

enum IntensityThresholdCalculation

method to use for estimating the maximal intensity that is used for histogram calculation

Enumerator
MANUAL
AUTOMAXBYSTDEV
AUTOMAXBYPERCENT

Constructor & Destructor Documentation

◆ SignalToNoiseEstimatorMedian() [1/2]

SignalToNoiseEstimatorMedian ( )

inline

default constructor

References DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMaxInt(), Param::setMinFloat(), Param::setMinInt(), DefaultParamHandler::setName(), Param::setValidStrings(), and Param::setValue().

◆ SignalToNoiseEstimatorMedian() [2/2]

SignalToNoiseEstimatorMedian ( const SignalToNoiseEstimatorMedian< Container > & source )

inline

Copy Constructor.

References SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ ~SignalToNoiseEstimatorMedian()

~SignalToNoiseEstimatorMedian ( )

inlineoverride

Destructor.

Member Function Documentation

◆ computeSTN_()

void computeSTN_ ( const Container & c )

inlineoverrideprotected

Calculate signal-to-noise values for all data points given, by using a sliding window approach

Parameters

c	Raw data, usually an MSSpectrum

Exceptions

Throws Exception::InvalidValue

start progress estimation

◆ getHistogramRightmostPercent()

double getHistogramRightmostPercent ( ) const

inline

Returns the percentage where the median was found in the rightmost bin.

References SignalToNoiseEstimatorMedian< Container >::histogram_oob_percent_.

◆ getSparseWindowPercent()

double getSparseWindowPercent ( ) const

inline

Returns how many percent of the windows were sparse.

References SignalToNoiseEstimatorMedian< Container >::sparse_window_percent_.

◆ operator=()

SignalToNoiseEstimatorMedian& operator= ( const SignalToNoiseEstimatorMedian< Container > & source )

inline

References SignalToNoiseEstimator< Container >::operator=(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ updateMembers_()

void updateMembers_ ( )

inlineoverrideprotectedvirtual

overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed

Reimplemented from DefaultParamHandler.

Referenced by SignalToNoiseEstimatorMedian< Container >::operator=(), and SignalToNoiseEstimatorMedian< Container >::SignalToNoiseEstimatorMedian().

Member Data Documentation

◆ auto_max_percentile_

double auto_max_percentile_

protected

parameter for initial automatic estimation of "max_intensity_" percentile or a stdev

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ auto_max_stdev_Factor_

double auto_max_stdev_Factor_

protected

parameter for initial automatic estimation of "max_intensity_": a stdev multiplier

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ auto_mode_

int auto_mode_

protected

determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ bin_count_

int bin_count_

protected

number of bins in the histogram

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ histogram_oob_percent_

double histogram_oob_percent_

protected

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::getHistogramRightmostPercent().

◆ max_intensity_

double max_intensity_

protected

maximal intensity considered during binning (values above get discarded)

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ min_required_elements_

int min_required_elements_

protected

minimal number of elements a window needs to cover to be used

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ noise_for_empty_window_

double noise_for_empty_window_

protected

used as noise value for windows which cover less than "min_required_elements_" use a very high value if you want to get a low S/N result

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ sparse_window_percent_

double sparse_window_percent_

protected

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::getSparseWindowPercent().

◆ win_len_

double win_len_

protected

range of data points which belong to a window in Thomson

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

◆ write_log_messages_

bool write_log_messages_

protected

Referenced by SignalToNoiseEstimatorMedian< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

Public Types

Public Member Functions

Assignment

Additional Inherited Members

Detailed Description

template<typename Container = MSSpectrum> class OpenMS::SignalToNoiseEstimatorMedian< Container >

Member Typedef Documentation

◆ GaussianEstimate

◆ PeakIterator

◆ PeakType

Member Enumeration Documentation

◆ IntensityThresholdCalculation

Constructor & Destructor Documentation

◆ SignalToNoiseEstimatorMedian() [1/2]

◆ SignalToNoiseEstimatorMedian() [2/2]

◆ ~SignalToNoiseEstimatorMedian()

Member Function Documentation

◆ computeSTN_()

◆ getHistogramRightmostPercent()

◆ getSparseWindowPercent()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ auto_max_percentile_

◆ auto_max_stdev_Factor_

◆ auto_mode_

◆ bin_count_

◆ histogram_oob_percent_

◆ max_intensity_

◆ min_required_elements_

◆ noise_for_empty_window_

◆ sparse_window_percent_

◆ win_len_

◆ write_log_messages_

template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimatorMedian< Container >